Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018299.1 Corchorus olitorius cultivar O-4 contig18332, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7960
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1894 original size:17 final size:16
Alignment explanation
Indices: 1872--1903 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1862 GGGTGTCTAG
1872 TTTTTCTTTCTTTTTCT
1 TTTTTCTTT-TTTTTCT
1889 TTTTTCTTTTTTTTC
1 TTTTTCTTTTTTTTC
1904 CAGGTTATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTCTTTTTTTTCT
Found at i:2560 original size:28 final size:27
Alignment explanation
Indices: 2520--2616 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 27
2510 GGTGTCCCTG
* *
2520 AAATGACCGAAATGCCCCTAGCCTAGCA
1 AAATGACCAAAATGCCCCTAG-GTAGCA
*
2548 AAATGACCAAAATGCCCCTGGATGTA-CA
1 AAATGACCAAAATGCCCCT--AGGTAGCA
2576 AAATGACCAAAATG-CCCTAGGTCATGCA
1 AAATGACCAAAATGCCCCTAGGT-A-GCA
2604 AAATGACCAAAAT
1 AAATGACCAAAAT
2617 AAAAGTAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
25 3 0.05
26 1 0.02
27 4 0.07
28 49 0.82
29 2 0.03
30 1 0.02
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTAGGTAGCA
Found at i:3766 original size:438 final size:436
Alignment explanation
Indices: 2990--3849 Score: 1043
Period size: 438 Copynumber: 2.0 Consensus size: 436
2980 CGCGTTCGCT
* * * *
2990 TTTATTTTTGTATTTTTTTTATATTTGTCCGATTAAGGTGATTCAAGTGTCTATTACAAGGTAAT
1 TTTATTTTTGTATTGTTTTTATATTTGTCCAATGAAGGTGATTCAAGTGTCTATTAAAAGGTAAT
* * * * ** * *
3055 TTCATGATCTACCATTTTCGTTTAGAACTCAAAAGTCAATTTTAATGTTTTGATTCTAAAAATTG
66 TTCATGATCTACAACTTTCATTAAGAACTCAAAAGTCAATTTTAATG-TTCAACTCTAAAAAATG
* * * * *
3120 CTTCTGAAATTTTGTGGTTTTGATTGCCGGTTAATTTAATATCGTATAATTTTTTGTCCACATCT
130 CTTCTGAAATTTGGTCGTTTCGATTGCCGGTTAATTTAATACCATATAATTTTTTGTCCACATCT
* * * * * * *
3185 CCGATTGAAATTATTGAAGTGTCGGATAAAAGGTTATTGCATGATTTACGACTTTTATGAAGGAC
195 CCAATTAAAATTATTCAAGTGTCGGATAAAAGGTTATTGCATAATCTACGACTTTCATGAAGAAC
* * * * * * *
3250 CTGAATGCTAAATTTGATCTACGAGTTTCGTTAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGA
260 CCGAAAGCTAAATTTAATCTACGAGTTTCATGAAGGATTCAAAAAGGAATTTTTATGTTTCAAGA
* **
3315 TCTCCATTAACAAACATTTTCTTATTTGAATTATTTATCAAATGGCCCTCATACTTTTCTACTTT
325 TCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTTT
*
3380 ATACTACTTAATTCTTTACAAATTCTATCTTAATCTAGCGTTTAAGC
390 ATACTACTTAATCCTTTACAAATTCTATCTTAATCTAGCGTTTAAGC
* * * * *
3427 TTTATTTTTTTATTCGTTTTTCTATTTGTCCAATGAAGTTGATTTATGTGTCTATTAAAAGGTAA
1 TTTATTTTTGTATT-GTTTTTATATTTGTCCAATGAAGGTGATTCAAGTGTCTATTAAAAGGTAA
* *
3492 TTTCATGATCTACAACTTTCATTAAGGACTCAAAAG-CAAATTTTTATG-TCAACT-TAAAAAAT
65 TTTCATGATCTACAACTTTCATTAAGAACTCAAAAGTC-AATTTTAATGTTCAACTCTAAAAAAT
** *
3554 GCTTCCT-AAATTTGGTCGTTTCGATTGTTGGTCT-ATTTAATACCATATAA-TTTTTGATTCAC
129 GCTT-CTGAAATTTGGTCGTTTCGATTGCCGGT-TAATTTAATACCATATAATTTTTTG-TCCAC
* * * *
3616 ATGTCTAATTAAAATTATTCAAGTGTCGGTTAAAAGGTTATTGTATAATCTACGACTTTCATGAA
191 ATCTCCAATTAAAATTATTCAAGTGTCGGATAAAAGGTTATTGCATAATCTACGACTTTCATGAA
* * *
3681 -AACCCGAAAG-TTAATTTAATCTACGAGTTTCATGAATGATTCAAAAATGAATTTTATATGTTT
256 GAACCCGAAAGCTAAATTTAATCTACGAGTTTCATGAAGGATTCAAAAAGGAATTTT-TATGTTT
* *
3744 CAAGATCTCCATTAATTAACAAATATTTTCTTATTTGAATTAGTTATCAAATCACCCTTATACTT
320 CAAGATCTCC----ATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTT
* * * *
3809 TTTTATTTTATGCTACTTAGTCCTTTACAAATTCTATCTTA
381 TTCTACTTTATACTACTTAATCCTTTACAAATTCTATCTTA
3850 CTCGATTTAA
Statistics
Matches: 355, Mismatches: 58, Indels: 19
0.82 0.13 0.04
Matches are distributed among these distances:
433 37 0.10
434 30 0.08
435 104 0.29
436 6 0.02
437 14 0.04
438 164 0.46
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (436 bp):
TTTATTTTTGTATTGTTTTTATATTTGTCCAATGAAGGTGATTCAAGTGTCTATTAAAAGGTAAT
TTCATGATCTACAACTTTCATTAAGAACTCAAAAGTCAATTTTAATGTTCAACTCTAAAAAATGC
TTCTGAAATTTGGTCGTTTCGATTGCCGGTTAATTTAATACCATATAATTTTTTGTCCACATCTC
CAATTAAAATTATTCAAGTGTCGGATAAAAGGTTATTGCATAATCTACGACTTTCATGAAGAACC
CGAAAGCTAAATTTAATCTACGAGTTTCATGAAGGATTCAAAAAGGAATTTTTATGTTTCAAGAT
CTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTTTA
TACTACTTAATCCTTTACAAATTCTATCTTAATCTAGCGTTTAAGC
Found at i:6277 original size:31 final size:32
Alignment explanation
Indices: 6241--6307 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
6231 TTGATTTAGG
* *
6241 AAATAGTGGCGTTT-TTTACAAAAACGCCGCT
1 AAATAGTGGCGTTTCTGTACAAAAACGCCACT
*
6272 AAATAGTGGCGTTTCTGTACGAAAACGCCACT
1 AAATAGTGGCGTTTCTGTACAAAAACGCCACT
6304 AAAT
1 AAAT
6308 GTACAGAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 14 0.44
32 18 0.56
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (32 bp):
AAATAGTGGCGTTTCTGTACAAAAACGCCACT
Done.